What is viral-ngs AGENTS.md?

Repository instructions for developing viral-ngs, a collection of tools for analysing viral genetic sequencing data. It uses a monorepo, meaning several related tools are kept in one repository, and Docker-based development.

Use it when changing viral-ngs utilities, assembly, classification, phylogenetics, or related Docker and development workflows.

It gives coding agents the project's expected setup and workflow instead of leaving them to infer how to build and test changes.

How broadinstitute/viral-ngs configures Codex and OpenCode

Reuse

Borrowing it

Nothing to install: this file belongs to broadinstitute/viral-ngs. Take a copy, put it at the same path in your own repository, and replace the rules that are about this project with yours.

Copy the file

curl -O https://raw.githubusercontent.com/broadinstitute/viral-ngs/main/AGENTS.md

Clone the repo

git clone --depth 1 https://github.com/broadinstitute/viral-ngs

Made for: Codex, OpenCode.

Wrote this? Show the measurements

A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.

README.md

[![agentmods](https://agentmods.dev/badge/instructions/broadinstitute/viral-ngs/agents-md/github.svg)](https://agentmods.dev/instructions/broadinstitute/viral-ngs/agents-md)

Your own site

<a href="https://agentmods.dev/instructions/broadinstitute/viral-ngs/agents-md"><img src="https://agentmods.dev/badge/instructions/broadinstitute/viral-ngs/agents-md/github.svg" alt="Measured on agentmods" height="20"></a>

Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.

Your own site · 80×15

<a href="https://agentmods.dev/instructions/broadinstitute/viral-ngs/agents-md"><img src="https://agentmods.dev/badge/instructions/broadinstitute/viral-ngs/agents-md.svg" alt="Reviewed on agentmods" width="80" height="20"></a>

Per session 5,441 This file is loaded in full into every session.

When invoked 5,441 The same file — it is already loaded in full.

Security scan A 0 findings. A grade says what 26 rules found in the file — not that it is safe.

Origin original No closer match found in the catalogue.

Token cost

What it costs to keep this loaded

Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.

Model	Per session	Once invoked
Fable 5.1	$0.05441	$0.05441
Opus 5.5	$0.02176	$0.02176
Sonnet 5.5	$0.01088	$0.01088
Haiku 4.5	$0.00544	$0.00544

Measured 21d ago against content hash d5c2c7d12a62, method: parsed. Prices are Anthropic first-party input rates as of 2026-10-07, from the pricing page.

Security

Grade A, and why

viral-ngs AGENTS.md scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 21d ago.

A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.

Nothing flagged

None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.

AGENTS.md · 610 lines

How it starts

The opening of the file, as written. The whole thing — 610 lines — stays where its author put it; the contents beside it link to each section on GitHub.

AGENTS.md

This document provides guidance for AI assistants (Claude Code, GitHub Copilot, etc.) working on this repository.

Overview

viral-ngs is a consolidated monorepo for viral NGS (Next-Generation Sequencing) analysis tools. It provides:

Core utilities: Read manipulation, Illumina demultiplexing, file handling, QC
Assembly: Genome assembly, scaffolding, gap filling
Classification: Metagenomic classification, taxonomy filtering, k-mer analysis
Phylogenetics: Variant calling, consensus generation, annotation

Related resources:

Command-line documentation: https://viral-ngs.readthedocs.org/
Higher-level pipelines: https://github.com/broadinstitute/viral-pipelines

Development Environment

Docker-Centric Development

Development is intentionally docker-centric. Developers need:

Docker
Git
Text/code editor

Development Workflow

Clone the repository:

git clone https://github.com/broadinstitute/viral-ngs.git

Run the container with local checkout mounted:

docker run -it --rm \
  -v $(pwd):/opt/viral-ngs/source \
  quay.io/broadinstitute/viral-ngs:main-core

If modifying conda dependencies, install them inside the container:
```
micromamba install <packages>
```

Test code interactively:

cd /opt/viral-ngs/source
pytest -rsxX -n auto tests/unit

Push changes to GitHub for automated CI testing

Running Tests

# Run all unit tests in the core image
docker run --rm \
  -v $(pwd):/opt/viral-ngs/source \
  quay.io/broadinstitute/viral-ngs:main-core \
  pytest -rsxX -n auto /opt/viral-ngs/source/tests/unit

# Run specific module tests
docker run --rm \
  -v $(pwd):/opt/viral-ngs/source \
  quay.io/broadinstitute/viral-ngs:main-classify \
  pytest -rsxX -n auto /opt/viral-ngs/source/tests/unit/classify

Important: Testing source code changes requires re-installing the package. The -v mount makes your local files visible on disk, but viral_ngs is already installed as a package inside the container image. Python imports resolve to the installed copy, not your mounted source files. If you've modified files under src/viral_ngs/, you must re-install before running tests:

Read the full file on GitHub · 610 lines

Changes

What this file has done since we first saw it

Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.

21d ago Changed · +85 tokens per session d5c2c7d12a62
1mo ago Changed · -6 tokens per session aec2cc7285d5
2mo ago Changed · +4 tokens per session 4e2714952441
2mo ago First seen · 610 lines · 5,358 tokens per session scan A d17caefa5790

Subscribe to this mod's changes

viral-ngs AGENTS.md is an instructions file published in the GitHub repository broadinstitute/viral-ngs (198 stars, last pushed yesterday), licensed MIT. It adds 5,441 tokens to every session, about $0.0218 per session on Opus 5.5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-30.

genome genome-assembly genome-sequencing genomics viral viral-ngs

viral-ngs AGENTS.md next to 6 instructions from other repositories
Mod	Type	Stars	Last push	Licence	Scan	Tokens	Works with
viral-ngs AGENTS.mdbroadinstitute/viral-ngs	Instructions file	198	yesterday	MIT	A	5,441	Codex, OpenCode
vscode buildNext.instructions.mdmicrosoft/vscode	Instructions file	195k	yesterday	MIT	A	9,719	GitHub Copilot
next.js AGENTS.mdvercel/next.js	Instructions file	143k	today	MIT	A	7,461	Codex, OpenCode
langchain AGENTS.mdlangchain-ai/langchain	Instructions file	149k	yesterday	MIT	A	4,680	Codex, OpenCode
vscode oss-third-party-notices.instructions.mdmicrosoft/vscode	Instructions file	195k	yesterday	MIT	A	5,516	GitHub Copilot
vscode copilot-instructions.mdmicrosoft/vscode	Instructions file	195k	yesterday	MIT	A	3,093	GitHub Copilot
deepseek-harness AGENTS.mddeepseek-ai/deepseek-harness	Instructions file	274k	2d ago	MIT	A	4,313	Codex, OpenCode

viral-ngs: Instructions file for Codex